Imputation Report For Cohort: Group1

Per chromosome imputation report for cohort Group1.

Chromosome index, 23 in total. Skip to the section for a particular chromosome using the buttons below.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X

Cohort Metadata

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Information captured during the processing of this cohort.

Property Value
FORMAT MINIMAC2

UPLOADED 31.5.2021

Genome-Wide

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A: Alternate Allele Frequency: Genome-Wide

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 7206299 61.045
0.1 1217154 10.311
0.2 808657 6.850
0.3 618825 5.242
0.4 496358 4.205
0.5 408199 3.458
0.6 347229 2.941
0.7 293101 2.483
0.8 246063 2.084
0.9 163056 1.381
Total 11804941 100.000

B: Imputation INFO Score: Genome-Wide

Variants binned by imputation INFO score

INFO Score Count %
0.3 320124 2.712
0.4 341746 2.895
0.5 430708 3.649
0.6 657091 5.566
0.7 1041515 8.823
0.8 1756587 14.880
0.9 7228502 61.233
1.0 28668 0.243
Total 11804941 100.000

Chromosome 1

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 547835 61.5312
0.1 89887 10.0958
0.2 57402 6.4472
0.3 45924 5.1580
0.4 37597 4.2228
0.5 30402 3.4147
0.6 27328 3.0694
0.7 21847 2.4538
0.8 18652 2.0949
0.9 13463 1.5121
Total 890337

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 25256 2.8367
0.4 26183 2.9408
0.5 33282 3.7381
0.6 50585 5.6816
0.7 80223 9.0104
0.8 134556 15.1129
0.9 538291 60.4592
1.0 1961 0.2203
Total 890337

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 2

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 599161 61.5987
0.1 101636 10.4490
0.2 64623 6.6438
0.3 50350 5.1764
0.4 38242 3.9316
0.5 32124 3.3026
0.6 29075 2.9891
0.7 22781 2.3421
0.8 21154 2.1748
0.9 13539 1.3919
Total 972685

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 25532 2.6249
0.4 27549 2.8323
0.5 33386 3.4324
0.6 50924 5.2354
0.7 82457 8.4773
0.8 141611 14.5588
0.9 608974 62.6075
1.0 2252 0.2315
Total 972685

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 3

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 503678 60.9229
0.1 87367 10.5676
0.2 56248 6.8035
0.3 42532 5.1445
0.4 34735 4.2014
0.5 29219 3.5342
0.6 24753 2.9940
0.7 20374 2.4644
0.8 16736 2.0243
0.9 11104 1.3431
Total 826746

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 21536 2.6049
0.4 22665 2.7415
0.5 28263 3.4186
0.6 43580 5.2713
0.7 70689 8.5503
0.8 119657 14.4732
0.9 518040 62.6601
1.0 2316 0.2801
Total 826746

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 4

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 500120 60.3197
0.1 81317 9.8077
0.2 60192 7.2598
0.3 45757 5.5188
0.4 33589 4.0512
0.5 27601 3.3290
0.6 25000 3.0153
0.7 21926 2.6445
0.8 19956 2.4069
0.9 13658 1.6473
Total 829116

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 20642 2.4896
0.4 22159 2.6726
0.5 27962 3.3725
0.6 42232 5.0936
0.7 69216 8.3482
0.8 119911 14.4625
0.9 525378 63.3660
1.0 1616 0.1949
Total 829116

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 5

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 466444 61.6107
0.1 76336 10.0829
0.2 52145 6.8876
0.3 40115 5.2986
0.4 31571 4.1701
0.5 24957 3.2965
0.6 22185 2.9303
0.7 18511 2.4450
0.8 15347 2.0271
0.9 9472 1.2511
Total 757083

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 19423 2.5655
0.4 20444 2.7004
0.5 25519 3.3707
0.6 39305 5.1916
0.7 63240 8.3531
0.8 108124 14.2817
0.9 478849 63.2492
1.0 2179 0.2878
Total 757083

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 6

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 455063 60.5522
0.1 79071 10.5214
0.2 52713 7.0142
0.3 40753 5.4227
0.4 32713 4.3529
0.5 26387 3.5111
0.6 21899 2.9140
0.7 17772 2.3648
0.8 15079 2.0065
0.9 10072 1.3402
Total 751522

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 17810 2.3699
0.4 18605 2.4756
0.5 22930 3.0511
0.6 35134 4.6750
0.7 56158 7.4726
0.8 96863 12.8889
0.9 499264 66.4337
1.0 4758 0.6331
Total 751522

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 7

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 403104 60.6249
0.1 68447 10.2941
0.2 48427 7.2832
0.3 35171 5.2895
0.4 29621 4.4549
0.5 23629 3.5537
0.6 18868 2.8377
0.7 15855 2.3845
0.8 12604 1.8956
0.9 9189 1.3820
Total 664915

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 17744 2.6686
0.4 18556 2.7907
0.5 23520 3.5373
0.6 36488 5.4876
0.7 58537 8.8037
0.8 98323 14.7873
0.9 410599 61.7521
1.0 1148 0.1727
Total 664915

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 8

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 395977 61.5019
0.1 64862 10.0742
0.2 44860 6.9675
0.3 31946 4.9618
0.4 27650 4.2945
0.5 22651 3.5181
0.6 18438 2.8637
0.7 15888 2.4677
0.8 13288 2.0639
0.9 8285 1.2868
Total 643845

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 16822 2.6127
0.4 18286 2.8401
0.5 22441 3.4855
0.6 33312 5.1739
0.7 54022 8.3905
0.8 91399 14.1958
0.9 405739 63.0181
1.0 1824 0.2833
Total 643845

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 9

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 307800 61.4667
0.1 55164 11.0161
0.2 32490 6.4882
0.3 25233 5.0390
0.4 20477 4.0892
0.5 16167 3.2285
0.6 14541 2.9038
0.7 11845 2.3654
0.8 9815 1.9600
0.9 7227 1.4432
Total 500759

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 13608 2.7175
0.4 14175 2.8307
0.5 17406 3.4759
0.6 27802 5.5520
0.7 45026 8.9916
0.8 75930 15.1630
0.9 306137 61.1346
1.0 675 0.1348
Total 500759

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 10

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 348878 60.6251
0.1 60094 10.4426
0.2 40186 6.9832
0.3 28433 4.9408
0.4 25343 4.4039
0.5 20778 3.6106
0.6 16672 2.8971
0.7 14265 2.4789
0.8 12772 2.2194
0.9 8047 1.3983
Total 575468

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 14213 2.4698
0.4 15286 2.6563
0.5 19006 3.3027
0.6 28720 4.9907
0.7 47410 8.2385
0.8 84393 14.6651
0.9 365311 63.4807
1.0 1129 0.1962
Total 575468

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 11

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 351679 61.0500
0.1 57668 10.0109
0.2 36584 6.3508
0.3 31056 5.3912
0.4 24637 4.2769
0.5 20528 3.5636
0.6 18376 3.1900
0.7 14195 2.4642
0.8 12601 2.1875
0.9 8727 1.5150
Total 576051

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 14265 2.4763
0.4 14464 2.5109
0.5 17905 3.1082
0.6 29265 5.0803
0.7 49471 8.5880
0.8 84042 14.5893
0.9 364864 63.3388
1.0 1775 0.3081
Total 576051

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 12

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 335336 61.1449
0.1 55733 10.1623
0.2 35698 6.5091
0.3 29802 5.4341
0.4 24023 4.3803
0.5 18941 3.4537
0.6 15691 2.8611
0.7 12679 2.3119
0.8 12796 2.3332
0.9 7729 1.4093
Total 548428

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 14335 2.6138
0.4 15353 2.7995
0.5 19306 3.5202
0.6 29239 5.3314
0.7 47692 8.6961
0.8 81507 14.8619
0.9 339827 61.9638
1.0 1169 0.2132
Total 548428

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 13

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 252967 60.0544
0.1 42959 10.1985
0.2 28152 6.6833
0.3 22830 5.4198
0.4 17214 4.0866
0.5 15861 3.7654
0.6 12687 3.0119
0.7 11368 2.6988
0.8 9625 2.2850
0.9 7567 1.7964
Total 421230

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 10665 2.5319
0.4 11308 2.6845
0.5 13975 3.3177
0.6 21938 5.2081
0.7 36328 8.6243
0.8 60120 14.2725
0.9 265811 63.1035
1.0 1085 0.2576
Total 421230

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 14

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 225360 61.1662
0.1 39218 10.6444
0.2 25744 6.9873
0.3 18163 4.9297
0.4 15305 4.1540
0.5 11643 3.1601
0.6 9989 2.7112
0.7 9574 2.5985
0.8 7715 2.0940
0.9 5728 1.5547
Total 368439

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 9648 2.6186
0.4 10025 2.7209
0.5 12805 3.4755
0.6 19918 5.4061
0.7 31315 8.4994
0.8 53791 14.5997
0.9 230266 62.4977
1.0 671 0.1821
Total 368439

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 15

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 200558 61.3295
0.1 32285 9.8726
0.2 22719 6.9473
0.3 17282 5.2847
0.4 13678 4.1827
0.5 11867 3.6289
0.6 8875 2.7139
0.7 7834 2.3956
0.8 6802 2.0800
0.9 5117 1.5648
Total 327017

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 9764 2.9858
0.4 10936 3.3442
0.5 14005 4.2827
0.6 20565 6.2887
0.7 30915 9.4536
0.8 51404 15.7191
0.9 188941 57.7771
1.0 487 0.1489
Total 327017

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 16

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 219924 61.7102
0.1 37324 10.4730
0.2 22878 6.4195
0.3 18914 5.3072
0.4 14273 4.0050
0.5 12376 3.4727
0.6 10636 2.9844
0.7 9420 2.6432
0.8 6691 1.8775
0.9 3946 1.1072
Total 356382

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 10176 2.8554
0.4 11351 3.1851
0.5 14196 3.9834
0.6 23117 6.4866
0.7 36687 10.2943
0.8 61945 17.3816
0.9 198572 55.7189
1.0 338 0.0948
Total 356382

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 17

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 186903 61.0375
0.1 30482 9.9546
0.2 22899 7.4782
0.3 15799 5.1595
0.4 12992 4.2428
0.5 11416 3.7282
0.6 8981 2.9330
0.7 8023 2.6201
0.8 5784 1.8889
0.9 2931 0.9572
Total 306210

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 10161 3.3183
0.4 11530 3.7654
0.5 15377 5.0217
0.6 22066 7.2062
0.7 33041 10.7903
0.8 51728 16.8930
0.9 161909 52.8752
1.0 398 0.1300
Total 306210

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 18

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 197652 60.4206
0.1 34190 10.4516
0.2 23586 7.2100
0.3 17549 5.3646
0.4 13970 4.2705
0.5 11147 3.4075
0.6 8972 2.7427
0.7 8473 2.5901
0.8 6777 2.0717
0.9 4811 1.4707
Total 327127

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 9559 2.9221
0.4 9756 2.9823
0.5 13379 4.0898
0.6 20193 6.1728
0.7 30613 9.3581
0.8 51927 15.8737
0.9 191258 58.4660
1.0 442 0.1351
Total 327127

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 19

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 152491 60.3841
0.1 29173 11.5521
0.2 19004 7.5253
0.3 13012 5.1526
0.4 9659 3.8248
0.5 8987 3.5587
0.6 6982 2.7648
0.7 5992 2.3727
0.8 4643 1.8386
0.9 2592 1.0264
Total 252535

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 7928 3.1394
0.4 9305 3.6846
0.5 12531 4.9621
0.6 18816 7.4508
0.7 27942 11.0646
0.8 43959 17.4071
0.9 131599 52.1112
1.0 455 0.1802
Total 252535

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 20

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 158874 61.4177
0.1 27379 10.5842
0.2 17762 6.8665
0.3 13664 5.2822
0.4 11040 4.2679
0.5 8826 3.4120
0.6 7641 2.9539
0.7 5931 2.2928
0.8 4665 1.8034
0.9 2896 1.1195
Total 258678

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 7360 2.8452
0.4 7708 2.9798
0.5 10549 4.0780
0.6 16386 6.3345
0.7 25257 9.7639
0.8 41642 16.0980
0.9 149486 57.7884
1.0 290 0.1121
Total 258678

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 21

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 90190 58.7385
0.1 15933 10.3768
0.2 10515 6.8482
0.3 8531 5.5560
0.4 7459 4.8579
0.5 5994 3.9037
0.6 4942 3.2186
0.7 4633 3.0174
0.8 3885 2.5302
0.9 1463 0.9528
Total 153545

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 4470 2.9112
0.4 4608 3.0011
0.5 6455 4.2040
0.6 9979 6.4991
0.7 14880 9.6910
0.8 24890 16.2102
0.9 88077 57.3623
1.0 186 0.1211
Total 153545

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 22

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 91651 60.7628
0.1 15815 10.4850
0.2 10903 7.2285
0.3 8186 5.4272
0.4 6623 4.3909
0.5 5318 3.5257
0.6 4528 3.0020
0.7 3882 2.5737
0.8 2617 1.7350
0.9 1311 0.8692
Total 150834

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 5032 3.3361
0.4 5445 3.6099
0.5 6848 4.5401
0.6 11019 7.3054
0.7 15840 10.5016
0.8 25721 17.0525
0.9 80781 53.5562
1.0 148 0.0981
Total 150834

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome X

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 214654 62.0407
0.1 34814 10.0622
0.2 22927 6.6265
0.3 17823 5.1513
0.4 13947 4.0311
0.5 11380 3.2891
0.6 10170 2.9394
0.7 10033 2.8998
0.8 6059 1.7512
0.9 4182 1.2087
Total 345989

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 14175 4.0970
0.4 16049 4.6386
0.5 19662 5.6828
0.6 26508 7.6615
0.7 34556 9.9876
0.8 53144 15.3600
0.9 180529 52.1777
1.0 1366 0.3948
Total 345989

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering